PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Translating genomics into practice for real-time surveillance and response to carbapenemase-producing Enterobacteriaceae: evidence from a complex multi-institutional KPC outbreak
items: Developmental effects of environmental light on male nuptial coloration in Lake Victoria cichlid fish
items: Formononetin inhibits lipopolysaccharide-induced release of high mobility group box 1 by upregulating SIRT1 in a PPARδ-dependent manner
items: A historical legacy of antibiotic utilization on bacterial seed banks in sediments
items: Effect of dark sweet cherry powder consumption on the gut microbiota, short-chain fatty acids, and biomarkers of gut health in obese db/db mice
items: Sex differences in the use of social information emerge under conditions of risk
items: Resistance strategies of Phragmites australis (common reed) to Pb pollution in flood and drought conditions
items: Profiling of subgingival plaque biofilm microbiota in female adult patients with clear aligners: a three-month prospective study
items: A gene expression-based risk model reveals prognosis of gastric cancer
items: Heteroassociative storage of hippocampal pattern sequences in the CA3 subregion

Translating genomics into practice for real-time surveillance and response to carbapenemase-producing Enterobacteriaceae: evidence from a complex multi-institutional KPC outbreak
type: item
type: AcademicArticle
description: Background Until recently, Klebsiella pneumoniae carbapenemase (KPC)-producing Enterobacteriaceae were rarely identified in Australia. Following an increase in the number of incident cases across the state of Victoria, we undertook a real-time combined genomic and epidemiological investigation. The scope of this study included identifying risk factors and routes of transmission, and investigating the utility of genomics to enhance traditional field epidemiology for informing management of established widespread outbreaks. Methods All KPC-producing Enterobacteriaceae isolates referred to the state reference laboratory from 2012 onwards were included. Whole-genome sequencing was performed in parallel with a detailed descriptive epidemiological investigation of each case, using Illumina sequencing on each isolate. This was complemented with PacBio long-read sequencing on selected isolates to establish high-quality reference sequences and interrogate characteristics of KPC-encoding plasmids. Results Initial investigations indicated that the outbreak was widespread, with 86 KPC-producing Enterobacteriaceae isolates (K. pneumoniae 92%) identified from 35 different locations across metropolitan and rural Victoria between 2012 and 2015. Initial combined analyses of the epidemiological and genomic data resolved the outbreak into distinct nosocomial transmission networks, and identified healthcare facilities at the epicentre of KPC transmission. New cases were assigned to transmission networks in real-time, allowing focussed infection control efforts. PacBio sequencing confirmed a secondary transmission network arising from inter-species plasmid transmission. Insights from Bayesian transmission inference and analyses of within-host diversity informed the development of state-wide public health and infection control guidelines, including interventions such as an intensive approach to screening contacts following new case detection to minimise unrecognised colonisation. Conclus…
format: application/pdf
format: text/html
creator: Jason C. Kwong
creator: Courtney R. Lane
creator: Finn Romanes
creator: Anders Gonçalves da Silva
creator: Marion Easton
creator: Katie Cronin
creator: Mary Jo Waters
creator: Takehiro Tomita
creator: Kerrie Stevens
creator: Mark B. Schultz
creator: Sarah L. Baines
creator: Norelle L. Sherry
creator: Glen P. Carter
creator: Andre Mu
creator: Michelle Sait
creator: Susan A. Ballard
creator: Torsten Seemann
creator: Timothy P. Stinear
creator: Benjamin P. Howden
subject: Genomics
subject: Microbiology
subject: Epidemiology
subject: Infectious Diseases
subject: Public Health
description: doi:10.7717/peerj.4210
publisher: PeerJ Inc.
rights: © 2018 Kwong et al.
abstract: Background Until recently, Klebsiella pneumoniae carbapenemase (KPC)-producing Enterobacteriaceae were rarely identified in Australia. Following an increase in the number of incident cases across the state of Victoria, we undertook a real-time combined genomic and epidemiological investigation. The scope of this study included identifying risk factors and routes of transmission, and investigating the utility of genomics to enhance traditional field epidemiology for informing management of established widespread outbreaks. Methods All KPC-producing Enterobacteriaceae isolates referred to the state reference laboratory from 2012 onwards were included. Whole-genome sequencing was performed in parallel with a detailed descriptive epidemiological investigation of each case, using Illumina sequencing on each isolate. This was complemented with PacBio long-read sequencing on selected isolates to establish high-quality reference sequences and interrogate characteristics of KPC-encoding plasmids. Results Initial investigations indicated that the outbreak was widespread, with 86 KPC-producing Enterobacteriaceae isolates (K. pneumoniae 92%) identified from 35 different locations across metropolitan and rural Victoria between 2012 and 2015. Initial combined analyses of the epidemiological and genomic data resolved the outbreak into distinct nosocomial transmission networks, and identified healthcare facilities at the epicentre of KPC transmission. New cases were assigned to transmission networks in real-time, allowing focussed infection control efforts. PacBio sequencing confirmed a secondary transmission network arising from inter-species plasmid transmission. Insights from Bayesian transmission inference and analyses of within-host diversity informed the development of state-wide public health and infection control guidelines, including interventions such as an intensive approach to screening contacts following new case detection to minimise unrecognised colonisation. Conclus…
bibliographic citation: Kwong et al. (2018) Translating genomics into practice for real-time surveillance and response to carbapenemase-producing Enterobacteriaceae: evidence from a complex multi-institutional KPC outbreak. PeerJ 6:e4210 https://doi.org/10.7717/peerj.4210
date submitted: 2017-10-12
date accepted: 2017-12-09
issued: 2018-01-03
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kwong
  given name: Jason C.
author list: Agent
  family name: Lane
  given name: Courtney R.
author list: Agent
  family name: Romanes
  given name: Finn
author list: Agent
  family name: Gonçalves da Silva
  given name: Anders
author list: Agent
  family name: Easton
  given name: Marion
author list: Agent
  family name: Cronin
  given name: Katie
author list: Agent
  family name: Waters
  given name: Mary Jo
author list: Agent
  family name: Tomita
  given name: Takehiro
author list: Agent
  family name: Stevens
  given name: Kerrie
author list: Agent
  family name: Schultz
  given name: Mark B.
author list: Agent
  family name: Baines
  given name: Sarah L.
author list: Agent
  family name: Sherry
  given name: Norelle L.
author list: Agent
  family name: Carter
  given name: Glen P.
author list: Agent
  family name: Mu
  given name: Andre
author list: Agent
  family name: Sait
  given name: Michelle
author list: Agent
  family name: Ballard
  given name: Susan A.
author list: Agent
  family name: Seemann
  given name: Torsten
author list: Agent
  family name: Stinear
  given name: Timothy P.
author list: Agent
  family name: Howden
  given name: Benjamin P.
doi: 10.7717/peerj.4210
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-01-03
copyright: © 2018 Kwong et al.
attribution name: Kwong et al.

Developmental effects of environmental light on male nuptial coloration in Lake Victoria cichlid fish
type: item
type: AcademicArticle
description: Background Efficient communication requires that signals are well transmitted and perceived in a given environment. Natural selection therefore drives the evolution of different signals in different environments. In addition, environmental heterogeneity at small spatial or temporal scales may favour phenotypic plasticity in signaling traits, as plasticity may allow rapid adjustment of signal expression to optimize transmission. In this study, we explore signal plasticity in the nuptial coloration of Lake Victoria cichlids, Pundamilia pundamilia and Pundamilia nyererei. These two species differ in male coloration, which mediates species-assortative mating. They occur in adjacent depth ranges with different light environments. Given the close proximity of their habitats, overlapping at some locations, plasticity in male coloration could contribute to male reproductive success but interfere with reproductive isolation. Methods We reared P. pundamilia, P. nyererei, and their hybrids under light conditions mimicking the two depth ranges in Lake Victoria. From photographs, we quantified the nuptial coloration of males, spanning the entire visible spectrum. In experiment 1, we examined developmental colour plasticity by comparing sibling males reared in each light condition. In experiment 2, we assessed colour plasticity in adulthood, by switching adult males between conditions and tracking coloration for 100 days. Results We found that nuptial colour in Pundamilia did respond plastically to our light manipulations, but only in a limited hue range. Fish that were reared in light conditions mimicking the deeper habitat were significantly greener than those in conditions mimicking shallow waters. The species-specific nuptial colours (blue and red) did not change. When moved to the opposing light condition as adults, males did not change colour. Discussion Our results show that species-specific nuptial colours, which are subject to strong divergent selection by female choice,…
format: application/pdf
format: text/html
creator: Daniel Shane Wright
creator: Emma Rietveld
creator: Martine E. Maan
subject: Aquaculture, Fisheries and Fish Science
subject: Evolutionary Studies
subject: Freshwater Biology
description: doi:10.7717/peerj.4209
publisher: PeerJ Inc.
rights: © 2018 Wright et al.
abstract: Background Efficient communication requires that signals are well transmitted and perceived in a given environment. Natural selection therefore drives the evolution of different signals in different environments. In addition, environmental heterogeneity at small spatial or temporal scales may favour phenotypic plasticity in signaling traits, as plasticity may allow rapid adjustment of signal expression to optimize transmission. In this study, we explore signal plasticity in the nuptial coloration of Lake Victoria cichlids, Pundamilia pundamilia and Pundamilia nyererei. These two species differ in male coloration, which mediates species-assortative mating. They occur in adjacent depth ranges with different light environments. Given the close proximity of their habitats, overlapping at some locations, plasticity in male coloration could contribute to male reproductive success but interfere with reproductive isolation. Methods We reared P. pundamilia, P. nyererei, and their hybrids under light conditions mimicking the two depth ranges in Lake Victoria. From photographs, we quantified the nuptial coloration of males, spanning the entire visible spectrum. In experiment 1, we examined developmental colour plasticity by comparing sibling males reared in each light condition. In experiment 2, we assessed colour plasticity in adulthood, by switching adult males between conditions and tracking coloration for 100 days. Results We found that nuptial colour in Pundamilia did respond plastically to our light manipulations, but only in a limited hue range. Fish that were reared in light conditions mimicking the deeper habitat were significantly greener than those in conditions mimicking shallow waters. The species-specific nuptial colours (blue and red) did not change. When moved to the opposing light condition as adults, males did not change colour. Discussion Our results show that species-specific nuptial colours, which are subject to strong divergent selection by female choice,…
bibliographic citation: Wright et al. (2018) Developmental effects of environmental light on male nuptial coloration in Lake Victoria cichlid fish. PeerJ 6:e4209 https://doi.org/10.7717/peerj.4209
date submitted: 2017-09-27
date accepted: 2017-12-09
issued: 2018-01-03
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wright
  given name: Daniel Shane
author list: Agent
  family name: Rietveld
  given name: Emma
author list: Agent
  family name: Maan
  given name: Martine E.
doi: 10.7717/peerj.4209
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-01-03
copyright: ©2018 Wright et al.
attribution name: Wright et al.

Formononetin inhibits lipopolysaccharide-induced release of high mobility group box 1 by upregulating SIRT1 in a PPARδ-dependent manner
type: item
type: AcademicArticle
description: Background The release of high mobility group box 1 (HMGB1) induced by inflammatory signals acts as a cellular alarmin to trigger a chain of inflammatory responses. Although the inflammatory actions of HMGB1 are well studied, less is known about the therapeutic agents that can impede its release. This study investigated whether the isoflavonoid formononetin can modulate HMGB1 release in cellular inflammatory responses. Methods RAW264.7 murine macrophages were exposed to lipopolysaccharide (LPS) in the presence or absence of formononetin. The levels of HMGB1 release, sirtuin 1 (SIRT1) expression, and HMGB1 acetylation were analyzed by immunoblotting and real-time polymerase chain reaction. The effects of resveratrol and sirtinol, an activator and inhibitor of SIRT1, respectively, on LPS-induced HMGB1 release were also evaluated. Results Formononetin modulated cellular inflammatory responses by suppressing the release of HMGB1 by macrophages exposed to LPS. In RAW264.7 cells, formononetin significantly attenuated LPS-induced release of HMGB1 into the extracellular environment, which was accompanied by a reduction in its translocation from the nucleus to the cytoplasm. In addition, formononetin significantly induced mRNA and protein expression of SIRT1 in a peroxisome proliferator-activated receptor δ (PPARδ)-dependent manner. These effects of formononetin were dramatically attenuated in cells treated with small interfering RNA (siRNA) against PPARδ or with GSK0660, a specific inhibitor of PPARδ, indicating that PPARδ is involved in formononetin-mediated SIRT1 expression. In line with these effects, formononetin-mediated inhibition of HMGB1 release in LPS-treated cells was reversed by treatment with SIRT1-targeting siRNA or sirtinol, a SIRT1 inhibitor. By contrast, resveratrol, a SIRT1 activator, further potentiated the inhibitory effect of formononetin on LPS-induced HMGB1 release, revealing a possible mechanism by which formononetin regulates HMGB1 release through SI…
format: application/pdf
format: text/html
creator: Jung Seok Hwang
creator: Eun Sil Kang
creator: Sung Gu Han
creator: Dae-Seog Lim
creator: Kyung Shin Paek
creator: Chi-Ho Lee
creator: Han Geuk Seo
subject: Cell Biology
subject: Molecular Biology
description: doi:10.7717/peerj.4208
publisher: PeerJ Inc.
rights: © 2018 Hwang et al.
abstract: Background The release of high mobility group box 1 (HMGB1) induced by inflammatory signals acts as a cellular alarmin to trigger a chain of inflammatory responses. Although the inflammatory actions of HMGB1 are well studied, less is known about the therapeutic agents that can impede its release. This study investigated whether the isoflavonoid formononetin can modulate HMGB1 release in cellular inflammatory responses. Methods RAW264.7 murine macrophages were exposed to lipopolysaccharide (LPS) in the presence or absence of formononetin. The levels of HMGB1 release, sirtuin 1 (SIRT1) expression, and HMGB1 acetylation were analyzed by immunoblotting and real-time polymerase chain reaction. The effects of resveratrol and sirtinol, an activator and inhibitor of SIRT1, respectively, on LPS-induced HMGB1 release were also evaluated. Results Formononetin modulated cellular inflammatory responses by suppressing the release of HMGB1 by macrophages exposed to LPS. In RAW264.7 cells, formononetin significantly attenuated LPS-induced release of HMGB1 into the extracellular environment, which was accompanied by a reduction in its translocation from the nucleus to the cytoplasm. In addition, formononetin significantly induced mRNA and protein expression of SIRT1 in a peroxisome proliferator-activated receptor δ (PPARδ)-dependent manner. These effects of formononetin were dramatically attenuated in cells treated with small interfering RNA (siRNA) against PPARδ or with GSK0660, a specific inhibitor of PPARδ, indicating that PPARδ is involved in formononetin-mediated SIRT1 expression. In line with these effects, formononetin-mediated inhibition of HMGB1 release in LPS-treated cells was reversed by treatment with SIRT1-targeting siRNA or sirtinol, a SIRT1 inhibitor. By contrast, resveratrol, a SIRT1 activator, further potentiated the inhibitory effect of formononetin on LPS-induced HMGB1 release, revealing a possible mechanism by which formononetin regulates HMGB1 release through SI…
bibliographic citation: Hwang et al. (2018) Formononetin inhibits lipopolysaccharide-induced release of high mobility group box 1 by upregulating SIRT1 in a PPARδ-dependent manner. PeerJ 6:e4208 https://doi.org/10.7717/peerj.4208
date submitted: 2017-08-22
date accepted: 2017-12-09
issued: 2018-01-03
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hwang
  given name: Jung Seok
author list: Agent
  family name: Kang
  given name: Eun Sil
author list: Agent
  family name: Han
  given name: Sung Gu
author list: Agent
  family name: Lim
  given name: Dae-Seog
author list: Agent
  family name: Paek
  given name: Kyung Shin
author list: Agent
  family name: Lee
  given name: Chi-Ho
author list: Agent
  family name: Seo
  given name: Han Geuk
doi: 10.7717/peerj.4208
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-01-03
copyright: © 2018 Hwang et al.
attribution name: Hwang et al.

A historical legacy of antibiotic utilization on bacterial seed banks in sediments
type: item
type: AcademicArticle
description: The introduction of antibiotics for both medical and non-medical purposes has had a positive effect on human welfare and agricultural output in the past century. However, there is also an important ecological legacy regarding the use of antibiotics and the consequences of increased levels of these compounds in the environment as a consequence of their use and disposal. This legacy was investigated by quantifying two antibiotic resistance genes (ARG) conferring resistance to tetracycline (tet(W)) and sulfonamide (sul1) in bacterial seed bank DNA in sediments. The industrial introduction of antibiotics caused an abrupt increase in the total abundance of tet(W) and a steady increase in sul1. The abrupt change in tet(W) corresponded to an increase in relative abundance from ca. 1960 that peaked around 1976. This pattern of accumulation was highly correlated with the abundance of specific members of the seed bank community belonging to the phylum Firmicutes. In contrast, the relative abundance of sul1 increased after 1976. This correlated with a taxonomically broad spectrum of bacteria, reflecting sul1 dissemination through horizontal gene transfer. The accumulation patterns of both ARGs correspond broadly to the temporal scale of medical antibiotic use. Our results show that the bacterial seed bank can be used to look back at the historical usage of antibiotics and resistance prevalence.
format: application/pdf
format: text/html
creator: Laura Madueño
creator: Christophe Paul
creator: Thomas Junier
creator: Zhanna Bayrychenko
creator: Sevasti Filippidou
creator: Karin Beck
creator: Gilbert Greub
creator: Helmut Bürgmann
creator: Pilar Junier
subject: Ecology
subject: Microbiology
subject: Health Policy
subject: Public Health
subject: Natural Resource Management
description: doi:10.7717/peerj.4197
publisher: PeerJ Inc.
rights: © 2018 Madueño et al.
abstract: The introduction of antibiotics for both medical and non-medical purposes has had a positive effect on human welfare and agricultural output in the past century. However, there is also an important ecological legacy regarding the use of antibiotics and the consequences of increased levels of these compounds in the environment as a consequence of their use and disposal. This legacy was investigated by quantifying two antibiotic resistance genes (ARG) conferring resistance to tetracycline (tet(W)) and sulfonamide (sul1) in bacterial seed bank DNA in sediments. The industrial introduction of antibiotics caused an abrupt increase in the total abundance of tet(W) and a steady increase in sul1. The abrupt change in tet(W) corresponded to an increase in relative abundance from ca. 1960 that peaked around 1976. This pattern of accumulation was highly correlated with the abundance of specific members of the seed bank community belonging to the phylum Firmicutes. In contrast, the relative abundance of sul1 increased after 1976. This correlated with a taxonomically broad spectrum of bacteria, reflecting sul1 dissemination through horizontal gene transfer. The accumulation patterns of both ARGs correspond broadly to the temporal scale of medical antibiotic use. Our results show that the bacterial seed bank can be used to look back at the historical usage of antibiotics and resistance prevalence.
bibliographic citation: Madueño et al. (2018) A historical legacy of antibiotic utilization on bacterial seed banks in sediments. PeerJ 6:e4197 https://doi.org/10.7717/peerj.4197
date submitted: 2017-10-19
date accepted: 2017-12-05
issued: 2018-01-03
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Madueño
  given name: Laura
author list: Agent
  family name: Paul
  given name: Christophe
author list: Agent
  family name: Junier
  given name: Thomas
author list: Agent
  family name: Bayrychenko
  given name: Zhanna
author list: Agent
  family name: Filippidou
  given name: Sevasti
author list: Agent
  family name: Beck
  given name: Karin
author list: Agent
  family name: Greub
  given name: Gilbert
author list: Agent
  family name: Bürgmann
  given name: Helmut
author list: Agent
  family name: Junier
  given name: Pilar
doi: 10.7717/peerj.4197
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-01-03
copyright: ©2018 Madueño et al.
attribution name: Madueño et al.

Effect of dark sweet cherry powder consumption on the gut microbiota, short-chain fatty acids, and biomarkers of gut health in obese db/db mice
type: item
type: AcademicArticle
description: Cherries are fruits containing fiber and bioactive compounds (e.g., polyphenolics) with the potential of helping patients with diabetes and weight disorders, a phenomenon likely related to changes in the complex host-microbiota milieu. The objective of this study was to investigate the effect of cherry supplementation on the gut bacterial composition, concentrations of caecal short-chain fatty acids (SCFAs) and biomarkers of gut health using an in vivo model of obesity. Obese diabetic (db/db) mice received a supplemented diet with 10% cherry powder (supplemented mice, n = 12) for 12 weeks; obese (n = 10) and lean (n = 10) mice served as controls and received a standard diet without cherry. High-throughput sequencing of the 16S rRNA gene and quantitative real-time PCR (qPCR) were used to analyze the gut microbiota; SCFAs and biomarkers of gut health were also measured using standard techniques. According to 16S sequencing, supplemented mice harbored a distinct colonic microbiota characterized by a higher abundance of mucin-degraders (i.e., Akkermansia) and fiber-degraders (the S24-7 family) as well as lower abundances of Lactobacillus and Enterobacteriaceae. Overall this particular cherry-associated colonic microbiota did not resemble the microbiota in obese or lean controls based on the analysis of weighted and unweighted UniFrac distance metrics. qPCR confirmed some of the results observed in sequencing, thus supporting the notion that cherry supplementation can change the colonic microbiota. Moreover, the SCFAs detected in supplemented mice (caproate, methyl butyrate, propionate, acetate and valerate) exceeded those concentrations detected in obese and lean controls except for butyrate. Despite the changes in microbial composition and SCFAs, most of the assessed biomarkers of inflammation, oxidative stress, and intestinal health in colon tissues and mucosal cells were similar in all obese mice with and without supplementation. This paper shows that dietary supplem…
format: application/pdf
format: text/html
creator: Jose F. Garcia-Mazcorro
creator: Nara N. Lage
creator: Susanne Mertens-Talcott
creator: Stephen Talcott
creator: Boon Chew
creator: Scot E. Dowd
creator: Jorge R. Kawas
creator: Giuliana D. Noratto
subject: Biochemistry
subject: Microbiology
subject: Molecular Biology
subject: Diabetes and Endocrinology
subject: Gastroenterology and Hepatology
description: doi:10.7717/peerj.4195
publisher: PeerJ Inc.
rights: © 2018 Garcia-Mazcorro et al.
abstract: Cherries are fruits containing fiber and bioactive compounds (e.g., polyphenolics) with the potential of helping patients with diabetes and weight disorders, a phenomenon likely related to changes in the complex host-microbiota milieu. The objective of this study was to investigate the effect of cherry supplementation on the gut bacterial composition, concentrations of caecal short-chain fatty acids (SCFAs) and biomarkers of gut health using an in vivo model of obesity. Obese diabetic (db/db) mice received a supplemented diet with 10% cherry powder (supplemented mice, n = 12) for 12 weeks; obese (n = 10) and lean (n = 10) mice served as controls and received a standard diet without cherry. High-throughput sequencing of the 16S rRNA gene and quantitative real-time PCR (qPCR) were used to analyze the gut microbiota; SCFAs and biomarkers of gut health were also measured using standard techniques. According to 16S sequencing, supplemented mice harbored a distinct colonic microbiota characterized by a higher abundance of mucin-degraders (i.e., Akkermansia) and fiber-degraders (the S24-7 family) as well as lower abundances of Lactobacillus and Enterobacteriaceae. Overall this particular cherry-associated colonic microbiota did not resemble the microbiota in obese or lean controls based on the analysis of weighted and unweighted UniFrac distance metrics. qPCR confirmed some of the results observed in sequencing, thus supporting the notion that cherry supplementation can change the colonic microbiota. Moreover, the SCFAs detected in supplemented mice (caproate, methyl butyrate, propionate, acetate and valerate) exceeded those concentrations detected in obese and lean controls except for butyrate. Despite the changes in microbial composition and SCFAs, most of the assessed biomarkers of inflammation, oxidative stress, and intestinal health in colon tissues and mucosal cells were similar in all obese mice with and without supplementation. This paper shows that dietary supplem…
bibliographic citation: Garcia-Mazcorro et al. (2018) Effect of dark sweet cherry powder consumption on the gut microbiota, short-chain fatty acids, and biomarkers of gut health in obese db/db mice. PeerJ 6:e4195 https://doi.org/10.7717/peerj.4195
date submitted: 2017-10-12
date accepted: 2017-12-05
issued: 2018-01-03
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Garcia-Mazcorro
  given name: Jose F.
author list: Agent
  family name: Lage
  given name: Nara N.
author list: Agent
  family name: Mertens-Talcott
  given name: Susanne
author list: Agent
  family name: Talcott
  given name: Stephen
author list: Agent
  family name: Chew
  given name: Boon
author list: Agent
  family name: Dowd
  given name: Scot E.
author list: Agent
  family name: Kawas
  given name: Jorge R.
author list: Agent
  family name: Noratto
  given name: Giuliana D.
doi: 10.7717/peerj.4195
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-01-03
copyright: ©2018 Garcia-Mazcorro et al.
attribution name: Garcia-Mazcorro et al.

Sex differences in the use of social information emerge under conditions of risk
type: item
type: AcademicArticle
description: Social learning provides an effective route to gaining up-to-date information, particularly when information is costly to obtain asocially. Theoretical work predicts that the willingness to switch between using asocial and social sources of information will vary between individuals according to their risk tolerance. We tested the prediction that, where there are sex differences in risk tolerance, altering the variance of the payoffs of using asocial and social information differentially influences the probability of social information use by sex. In a computer-based task that involved building a virtual spaceship, men and women (N = 88) were given the option of using either asocial or social sources of information to improve their performance. When the asocial option was risky (i.e., the participant’s score could markedly increase or decrease) and the social option was safe (i.e., their score could slightly increase or remain the same), women, but not men, were more likely to use the social option than the asocial option. In all other conditions, both women and men preferentially used the asocial option to a similar degree. We therefore found both a sex difference in risk aversion and a sex difference in the preference for social information when relying on asocial information was risky, consistent with the hypothesis that levels of risk-aversion influence the use of social information.
format: application/pdf
format: text/html
creator: Charlotte O. Brand
creator: Gillian R. Brown
creator: Catharine P. Cross
subject: Animal Behavior
subject: Anthropology
subject: Evolutionary Studies
description: doi:10.7717/peerj.4190
publisher: PeerJ Inc.
rights: © 2018 Brand et al.
abstract: Social learning provides an effective route to gaining up-to-date information, particularly when information is costly to obtain asocially. Theoretical work predicts that the willingness to switch between using asocial and social sources of information will vary between individuals according to their risk tolerance. We tested the prediction that, where there are sex differences in risk tolerance, altering the variance of the payoffs of using asocial and social information differentially influences the probability of social information use by sex. In a computer-based task that involved building a virtual spaceship, men and women (N = 88) were given the option of using either asocial or social sources of information to improve their performance. When the asocial option was risky (i.e., the participant’s score could markedly increase or decrease) and the social option was safe (i.e., their score could slightly increase or remain the same), women, but not men, were more likely to use the social option than the asocial option. In all other conditions, both women and men preferentially used the asocial option to a similar degree. We therefore found both a sex difference in risk aversion and a sex difference in the preference for social information when relying on asocial information was risky, consistent with the hypothesis that levels of risk-aversion influence the use of social information.
bibliographic citation: Brand et al. (2018) Sex differences in the use of social information emerge under conditions of risk. PeerJ 6:e4190 https://doi.org/10.7717/peerj.4190
date submitted: 2017-08-29
date accepted: 2017-12-04
issued: 2018-01-03
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Brand
  given name: Charlotte O.
author list: Agent
  family name: Brown
  given name: Gillian R.
author list: Agent
  family name: Cross
  given name: Catharine P.
doi: 10.7717/peerj.4190
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-01-03
copyright: ©2018 Brand et al.
attribution name: Brand et al.

Resistance strategies of Phragmites australis (common reed) to Pb pollution in flood and drought conditions
type: item
type: AcademicArticle
description: Resistance strategies of clonal organs, and parent and offspring shoots of Phragmites australis (common reed) to heavy metal pollution in soils are not well known. To clarify the tolerance or resistance strategies in reeds, we conducted a pot experiment with five levels of Pb concentration (0∼4,500 mg kg−1) in flood and drought conditions. Lead toxicity had no inhibitory effect on the number of offspring shoots in flood environment; however, biomass accumulation, and photosynthetic and clonal growth parameters were inhibited in both water environment. At each treatment of Pb concentration, offspring shoots had greater biomass and higher photosynthesis indicators than parent shoots. The lowest Pb allocation was found in rhizomes. More of the Pb transported to above-ground parts tended to accumulate in parent shoots rather than in offspring shoots. Biomass and photosynthesis of offspring shoots, rhizome length, and the number of buds, rhizomes and offspring shoots in the flooded treatment were significantly greater than those in the drought treatment. Our results indicated that the tolerance strategies used by reeds, including higher biomass accumulation and photosynthesis in offspring shoots, low allocation of Pb in rhizomes and offspring shoots, and stable clonal growth, maintained the stability of population propagation and productivity, improving the resistance of reeds to Pb pollution in flood environment. However, the resistance or tolerance was significantly reduced by the synergistic effect of Pb and drought, which significantly inhibited biomass accumulation, photosynthesis, and clonal growth of reeds.
format: application/pdf
format: text/html
creator: Na Zhang
creator: Jinwei Zhang
creator: Zhiqiang Li
creator: Jing Chen
creator: Zhenhua Zhang
creator: Chunsheng Mu
subject: Ecotoxicology
subject: Environmental Contamination and Remediation
description: doi:10.7717/peerj.4188
publisher: PeerJ Inc.
rights: © 2018 Zhang et al.
abstract: Resistance strategies of clonal organs, and parent and offspring shoots of Phragmites australis (common reed) to heavy metal pollution in soils are not well known. To clarify the tolerance or resistance strategies in reeds, we conducted a pot experiment with five levels of Pb concentration (0∼4,500 mg kg−1) in flood and drought conditions. Lead toxicity had no inhibitory effect on the number of offspring shoots in flood environment; however, biomass accumulation, and photosynthetic and clonal growth parameters were inhibited in both water environment. At each treatment of Pb concentration, offspring shoots had greater biomass and higher photosynthesis indicators than parent shoots. The lowest Pb allocation was found in rhizomes. More of the Pb transported to above-ground parts tended to accumulate in parent shoots rather than in offspring shoots. Biomass and photosynthesis of offspring shoots, rhizome length, and the number of buds, rhizomes and offspring shoots in the flooded treatment were significantly greater than those in the drought treatment. Our results indicated that the tolerance strategies used by reeds, including higher biomass accumulation and photosynthesis in offspring shoots, low allocation of Pb in rhizomes and offspring shoots, and stable clonal growth, maintained the stability of population propagation and productivity, improving the resistance of reeds to Pb pollution in flood environment. However, the resistance or tolerance was significantly reduced by the synergistic effect of Pb and drought, which significantly inhibited biomass accumulation, photosynthesis, and clonal growth of reeds.
bibliographic citation: Zhang et al. (2018) Resistance strategies of Phragmites australis (common reed) to Pb pollution in flood and drought conditions. PeerJ 6:e4188 https://doi.org/10.7717/peerj.4188
date submitted: 2017-11-18
date accepted: 2017-12-03
issued: 2018-01-03
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Na
author list: Agent
  family name: Zhang
  given name: Jinwei
author list: Agent
  family name: Li
  given name: Zhiqiang
author list: Agent
  family name: Chen
  given name: Jing
author list: Agent
  family name: Zhang
  given name: Zhenhua
author list: Agent
  family name: Mu
  given name: Chunsheng
doi: 10.7717/peerj.4188
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-01-03
copyright: ©2018 Zhang et al.
attribution name: Zhang et al.

Profiling of subgingival plaque biofilm microbiota in female adult patients with clear aligners: a three-month prospective study
type: item
type: AcademicArticle
description: Background Clear aligners are well known for facilitating oral hygiene maintenance and decreasing susceptibility to periodontal diseases as compared to conventional fixed appliances. However, few research studies focus on the subgingival microbial community during clear aligner treatment (CAT). Hence, this study investigates changes of the subgingival microbial community and its association with clinical characteristics during the first three months of CAT. Methods Ten female patients with clear aligners were enrolled in this study. Subgingival plaque samples were obtained at three time points: before orthodontic treatment (T0), one month after orthodontic treatment (T1) and three months after orthodontic treatment (T2). DNA was then extracted from plaque samples and analyzed by 16S rRNA gene sequencing. Periodontal examinations, including plaque index (PI) and gingival bleeding index (GBI) measurements were also recorded. Results The plaque indices (PIs) and gingival bleeding indices (GBIs) were slightly increased at T1 and T2, but no statistically significant difference was found. The alpha diversity indices, including the ACE, Chao1, Shannon indices, all showed a declining trend without significance, and a rising trend in the Simpson diversity index was observed. The weighted UniFrac distance was significantly higher at T1 and T2 compared with T0. Principal Coordinates Analysis (PCoA) demonstrated that the communities at T0 tended to cluster apart from the communities at T1 and T2. The relative abundance of the phylum Firmicutes and genus Mycoplasma was significantly increased at T0 compared with T2. There was no significant difference in the relative abundance of periodontal pathogens at the genus and species levels or core microorganisms at the genus level. Conclusion A slightly decreasing microbial diversity with a significant change of microbial structure was found during the first three-month clear aligner treatment (CAT). However, subjects receiving clear a…
format: application/pdf
format: text/html
creator: Runzhi Guo
creator: Yunfei Zheng
creator: Hao Liu
creator: Xiaobei Li
creator: Lingfei Jia
creator: Weiran Li
subject: Microbiology
subject: Dentistry
description: doi:10.7717/peerj.4207
publisher: PeerJ Inc.
rights: © 2018 Guo et al.
abstract: Background Clear aligners are well known for facilitating oral hygiene maintenance and decreasing susceptibility to periodontal diseases as compared to conventional fixed appliances. However, few research studies focus on the subgingival microbial community during clear aligner treatment (CAT). Hence, this study investigates changes of the subgingival microbial community and its association with clinical characteristics during the first three months of CAT. Methods Ten female patients with clear aligners were enrolled in this study. Subgingival plaque samples were obtained at three time points: before orthodontic treatment (T0), one month after orthodontic treatment (T1) and three months after orthodontic treatment (T2). DNA was then extracted from plaque samples and analyzed by 16S rRNA gene sequencing. Periodontal examinations, including plaque index (PI) and gingival bleeding index (GBI) measurements were also recorded. Results The plaque indices (PIs) and gingival bleeding indices (GBIs) were slightly increased at T1 and T2, but no statistically significant difference was found. The alpha diversity indices, including the ACE, Chao1, Shannon indices, all showed a declining trend without significance, and a rising trend in the Simpson diversity index was observed. The weighted UniFrac distance was significantly higher at T1 and T2 compared with T0. Principal Coordinates Analysis (PCoA) demonstrated that the communities at T0 tended to cluster apart from the communities at T1 and T2. The relative abundance of the phylum Firmicutes and genus Mycoplasma was significantly increased at T0 compared with T2. There was no significant difference in the relative abundance of periodontal pathogens at the genus and species levels or core microorganisms at the genus level. Conclusion A slightly decreasing microbial diversity with a significant change of microbial structure was found during the first three-month clear aligner treatment (CAT). However, subjects receiving clear a…
bibliographic citation: Guo et al. (2018) Profiling of subgingival plaque biofilm microbiota in female adult patients with clear aligners: a three-month prospective study. PeerJ 6:e4207 https://doi.org/10.7717/peerj.4207
date submitted: 2017-09-13
date accepted: 2017-12-08
issued: 2018-01-02
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Guo
  given name: Runzhi
author list: Agent
  family name: Zheng
  given name: Yunfei
author list: Agent
  family name: Liu
  given name: Hao
author list: Agent
  family name: Li
  given name: Xiaobei
author list: Agent
  family name: Jia
  given name: Lingfei
author list: Agent
  family name: Li
  given name: Weiran
doi: 10.7717/peerj.4207
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-01-02
copyright: ©2018 Guo et al.
attribution name: Guo et al.

A gene expression-based risk model reveals prognosis of gastric cancer
type: item
type: AcademicArticle
description: Background The prognosis of gastric cancer is difficult to determine, although clinical indicators provide valuable evidence. Methods In this study, using screened biomarkers of gastric cancer in combination with random forest variable hunting and multivariable Cox regression, a risk score model was developed to predict the survival of gastric cancer. Survival difference between high/low-risk groups were compared. The relationship between risk score and other clinicopathological indicators was evaluated. Gene set enrichment analysis (GSEA) was used to identify pathways associated with risk scores. Results The patients with high risk scores (median overall survival: 20.2 months, 95% CI [16.9–26.0] months) tend to exhibit early events compared with those with low risk scores (median survival: 70.0 months, 95% CI [46.9–101] months, p = 1.80e–5). Further validation was implemented in another three independent datasets (GSE15459, GSE26253, GSE62254). Correlation analyses between clinical observations and risk scores were performed, and the results indicated that the risk score was not significantly associated with gender, age and primary tumor size but was significantly associated with grade and tumor stage. In addition, the risk score was also not influenced by radiation therapy. Cox multivariate regression and three-year survival nomogram suggest that the risk score is an important indicator of gastric cancer prognosis. GSEA was used to identified KEGG pathways significantly associated with risk score, and signaling pathways involved in focal adhesion and the TGF-beta signaling pathway were identified. Conclusion The risk score model successfully predicted the survival of 1,294 gastric cancer samples from four independent datasets and is among the most important indicators in clinical clinicopathological information for the prognosis of gastric cancer. To our knowledge, it is the first report to predict the survival of gastric cancer using optimized expression panel.
format: application/pdf
format: text/html
creator: Xiaorong Deng
creator: Qun Xiao
creator: Feng Liu
creator: Cihua Zheng
subject: Bioinformatics
subject: Gastroenterology and Hepatology
subject: Oncology
description: doi:10.7717/peerj.4204
publisher: PeerJ Inc.
rights: © 2018 Deng et al.
abstract: Background The prognosis of gastric cancer is difficult to determine, although clinical indicators provide valuable evidence. Methods In this study, using screened biomarkers of gastric cancer in combination with random forest variable hunting and multivariable Cox regression, a risk score model was developed to predict the survival of gastric cancer. Survival difference between high/low-risk groups were compared. The relationship between risk score and other clinicopathological indicators was evaluated. Gene set enrichment analysis (GSEA) was used to identify pathways associated with risk scores. Results The patients with high risk scores (median overall survival: 20.2 months, 95% CI [16.9–26.0] months) tend to exhibit early events compared with those with low risk scores (median survival: 70.0 months, 95% CI [46.9–101] months, p = 1.80e–5). Further validation was implemented in another three independent datasets (GSE15459, GSE26253, GSE62254). Correlation analyses between clinical observations and risk scores were performed, and the results indicated that the risk score was not significantly associated with gender, age and primary tumor size but was significantly associated with grade and tumor stage. In addition, the risk score was also not influenced by radiation therapy. Cox multivariate regression and three-year survival nomogram suggest that the risk score is an important indicator of gastric cancer prognosis. GSEA was used to identified KEGG pathways significantly associated with risk score, and signaling pathways involved in focal adhesion and the TGF-beta signaling pathway were identified. Conclusion The risk score model successfully predicted the survival of 1,294 gastric cancer samples from four independent datasets and is among the most important indicators in clinical clinicopathological information for the prognosis of gastric cancer. To our knowledge, it is the first report to predict the survival of gastric cancer using optimized expression panel.
bibliographic citation: Deng et al. (2018) A gene expression-based risk model reveals prognosis of gastric cancer. PeerJ 6:e4204 https://doi.org/10.7717/peerj.4204
date submitted: 2017-11-08
date accepted: 2017-12-08
issued: 2018-01-02
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Deng
  given name: Xiaorong
author list: Agent
  family name: Xiao
  given name: Qun
author list: Agent
  family name: Liu
  given name: Feng
author list: Agent
  family name: Zheng
  given name: Cihua
doi: 10.7717/peerj.4204
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-01-02
copyright: ©2018 Deng et al.
attribution name: Deng et al.

Heteroassociative storage of hippocampal pattern sequences in the CA3 subregion
type: item
type: AcademicArticle
description: Background Recent research suggests that the CA3 subregion of the hippocampus has properties of both autoassociative network, due to its ability to complete partial cues, tolerate noise, and store associations between memories, and heteroassociative one, due to its ability to store and retrieve sequences of patterns. Although there are several computational models of the CA3 as an autoassociative network, more detailed evaluations of its heteroassociative properties are missing. Methods We developed a model of the CA3 subregion containing 10,000 integrate-and-fire neurons with both recurrent excitatory and inhibitory connections, and which exhibits coupled oscillations in the gamma and theta ranges. We stored thousands of pattern sequences using a heteroassociative learning rule with competitive synaptic scaling. Results We showed that a purely heteroassociative network model can (i) retrieve pattern sequences from partial cues with external noise and incomplete connectivity, (ii) achieve homeostasis regarding the number of connections per neuron when many patterns are stored when using synaptic scaling, (iii) continuously update the set of retrievable patterns, guaranteeing that the last stored patterns can be retrieved and older ones can be forgotten. Discussion Heteroassociative networks with synaptic scaling rules seem sufficient to achieve many desirable features regarding connectivity homeostasis, pattern sequence retrieval, noise tolerance and updating of the set of retrievable patterns.
format: application/pdf
format: text/html
creator: Raphael Y. de Camargo
creator: Renan S. Recio
creator: Marcelo B. Reyes
subject: Computational Biology
subject: Neuroscience
description: doi:10.7717/peerj.4203
publisher: PeerJ Inc.
rights: © 2018 de Camargo et al.
abstract: Background Recent research suggests that the CA3 subregion of the hippocampus has properties of both autoassociative network, due to its ability to complete partial cues, tolerate noise, and store associations between memories, and heteroassociative one, due to its ability to store and retrieve sequences of patterns. Although there are several computational models of the CA3 as an autoassociative network, more detailed evaluations of its heteroassociative properties are missing. Methods We developed a model of the CA3 subregion containing 10,000 integrate-and-fire neurons with both recurrent excitatory and inhibitory connections, and which exhibits coupled oscillations in the gamma and theta ranges. We stored thousands of pattern sequences using a heteroassociative learning rule with competitive synaptic scaling. Results We showed that a purely heteroassociative network model can (i) retrieve pattern sequences from partial cues with external noise and incomplete connectivity, (ii) achieve homeostasis regarding the number of connections per neuron when many patterns are stored when using synaptic scaling, (iii) continuously update the set of retrievable patterns, guaranteeing that the last stored patterns can be retrieved and older ones can be forgotten. Discussion Heteroassociative networks with synaptic scaling rules seem sufficient to achieve many desirable features regarding connectivity homeostasis, pattern sequence retrieval, noise tolerance and updating of the set of retrievable patterns.
bibliographic citation: de Camargo et al. (2018) Heteroassociative storage of hippocampal pattern sequences in the CA3 subregion. PeerJ 6:e4203 https://doi.org/10.7717/peerj.4203
date submitted: 2017-06-14
date accepted: 2017-12-07
issued: 2018-01-02
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: de Camargo
  given name: Raphael Y.
author list: Agent
  family name: Recio
  given name: Renan S.
author list: Agent
  family name: Reyes
  given name: Marcelo B.
doi: 10.7717/peerj.4203
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-01-02
copyright: ©2018 de Camargo et al.
attribution name: de Camargo et al.

PeerJ
type: Periodical
uri: PeerJ
issn: 2167-8359